I'm trying to create a PCA plot with my data. I managed to create it with all my genes using the standard script:
genes.PCA<-PCAplot(genes(cuff), "PC1","PC2")

However, I would like to create the plot with a subset of those gene, e.g. the differentially expressed (DE) genes. I've created a subset for the DE genes as followed:gene_diff_data<-diffData(genes(cuff))
sig_gene_data<-subset(gene_diff_data, (significant=='yes'))
sig_genes<-getGenes(cuff, sig_gene_data$gene_id)